A5005143315- Genomics and Chromatin Dynamics
- Advanced Fluorescence Microscopy Techniques
- RNA Research and Splicing
- Teleoperation and Haptic Systems
- Cell Image Analysis Techniques
- CRISPR and Genetic Engineering
- COVID-19 and healthcare impacts
- Dark Matter and Cosmic Phenomena
- Body Contouring and Surgery
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Diffusion and Search Dynamics
- DNA and Nucleic Acid Chemistry
- DNA Repair Mechanisms
- Advanced biosensing and bioanalysis techniques
- BIM and Construction Integration
- Atomic and Subatomic Physics Research
- Ubiquitin and proteasome pathways
- Gene expression and cancer classification
- Bariatric Surgery and Outcomes
- Gene Regulatory Network Analysis
- Force Microscopy Techniques and Applications
- Particle Detector Development and Performance
- RNA regulation and disease
- NF-κB Signaling Pathways
Istituti di Ricovero e Cura a Carattere Scientifico
2018-2025
Vita-Salute San Raffaele University
2013-2024
Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele
2018-2024
IRCCS Ospedale San Raffaele
2013-2024
Michigan State University
2024
San Raffaele University of Rome
2015-2022
University of Birmingham
2020
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2014-2016
Imaging Center
2014
Politecnico di Milano
2009-2014
Live-cell measurement of protein binding to chromatin allows probing cellular biochemistry in physiological conditions, which are difficult mimic vitro. However, different studies have yielded widely discrepant predictions, and so it remains uncertain how make the measurements accurately. To establish a benchmark we measured transcription factor p53 by three approaches: fluorescence recovery after photobleaching (FRAP), correlation spectroscopy (FCS) single-molecule tracking (SMT). Using new...
Abstract Cells undergo tens of thousands DNA-damaging events each day. Defects in repairing double-stranded breaks (DSBs) can lead to genomic instability, contributing cancer, genetic disorders, immunological diseases, and developmental defects. Cohesin, a multi-subunit protein complex, plays crucial role both chromosome organization DNA repair by creating architectural loops through chromatin extrusion. However, the mechanisms which cohesin regulates these distinct processes are not fully...
Abstract Population-based assays have been employed extensively to investigate the interactions of transcription factors (TFs) with chromatin and are often interpreted in terms static sequential binding. However, fluorescence microscopy techniques reveal a more dynamic binding behaviour TFs live cells. Here we analyse strengths limitations vivo single-molecule tracking performed comprehensive analysis on intranuclear dwell times four steroid receptors number known cofactors. While absolute...
ER-PM contacts in nonclathrin endocytosis The epidermal growth factor receptor (EGFR) is internalized through both clathrin-mediated and (NCE). two pathways act concert to sustain EGFR signaling or its long-term attenuation. mechanistic underpinnings of EGFR-NCE are unclear. Caldieri et al. used a variety cell molecular biology approaches identify nine regulators (see the Perspective by Tan Anderson). They also identified an additional cargo pathway (CD147). One was endoplasmic reticulum...
Live-cell microscopy has highlighted that transcription factors bind transiently to chromatin but it is not clear if the duration of these binding interactions can be modulated in response an activation stimulus, and such modulation controlled by post-translational modifications factor. We address this question for tumor suppressor p53 combining live-cell single-molecule single cell situ measurements we show p53-binding kinetics are following genotoxic stress. The residence times on requires...
The cohesin complex mediates DNA-DNA interactions both between (sister chromatid cohesion) and within chromosomes (DNA looping). It has been suggested that intra-chromosome loops are generated by extrusion of DNAs through the lumen cohesin’s ring. Scc2 (Nipbl) stimulates ABC-like ATPase is essential for loading onto chromosomes. However, it possible stimulation also a post-loading function, example driving loop extrusion. Using fluorescence recovery after photobleaching (FRAP)...
Nuclear factors rapidly scan the genome for their targets, but role of nuclear organization in such search is uncharted. Here we analyzed how multiple explore chromatin, combining live-cell single-molecule tracking with multifocal structured illumination DNA density. We find that displaying higher bound fractions sample DNA-dense regions more exhaustively. Focusing on tumor-suppressor p53, demonstrate it searches targets by alternating between rapid diffusion interchromatin compartment and...
Spinocerebellar ataxia type 28 (SCA28) is a neurodegenerative disease caused by mutations of the mitochondrial protease AFG3L2. The SCA28 mouse model, which haploinsufficient for Afg3l2, exhibits progressive decline in motor function and displays dark degeneration Purkinje cells (PC-DCD) origin. Here, we determined that mitochondria cultured Afg3l2-deficient PCs ineffectively buffer evoked Ca2+ peaks, resulting enhanced cytoplasmic concentrations, subsequently triggers PC-DCD. This...
In vivo single molecule tracking has recently developed into a powerful technique for measuring and understanding the transient interactions of transcription factors (TF) with their chromatin response elements. However, this method still lacks solid foundation distinguishing between specific non-specific interactions. To address issue, we took advantage power molecular genetics yeast. Yeast TF Ace1p only five sites in genome thus serves as benchmark to distinguish from binding. Here, show...
Histones are the protein component of nucleosomes, which basic packing unit chromatin. However, histones also found in blood, both as components nucleosomes leaked out from dead cells, or expelled neutrophils active process NET formation. Circulating contribute to inflammation, and lethality sepsis, a hyperinflammatory conditions, by interacting with specific receptors, notably Toll-Like Receptor 4 (TLR4). Here we show that actively released LPS-activated macrophages association...
Transcription factors (TFs) regulate gene expression in both prokaryotes and eukaryotes by recognizing binding to specific DNA promoter sequences. In higher eukaryotes, it remains unclear how the duration of TF relates downstream transcriptional output. Here, we address this question for activator NF-κB (p65), live-cell single molecule imaging TF-DNA kinetics genome-wide quantification p65-mediated transcription. We used mutants p65, perturbing either domain (DBD) or protein-protein...
It is widely assumed that decreasing transcription factor DNA-binding affinity reduces initiation by diminishing occupancy of sequence-specific regulatory elements. However, in vivo factors find their binding sites while confronted with a large excess low-affinity degenerate motifs. Here, using the melanoma lineage survival oncogene MITF as model, we show act competitive reservoir from which are released mitogen-activated protein kinase (MAPK)-stimulated acetylation to promote increased...
The immobilization of cells in defined arrays (cell patterning) is a key step towards cell-based biosensors or other devices. While cell patterning usually achieved by modifying the surface on which only should adhere and leaving unmodified, we present here different approach are first coated with polyelectrolytes subsequently immobilized patterned surfaces. By coating, protected their interactions substrate modified such that simplified. We used microcontact printing to structure surfaces...